I'm using YourKit build-15088 to profile an Eclipse RCP running with OpenJDK 8 on Linux. The CPU tracing report shows that the time spent is inside java.lang.Thread.run(), but the stack trace is incomplete. The Callee List does not show the children of that method. I tried sampling instead of tracing and a similar result occurs.

I tried to change the CPU tracing settings by removing the walltime entries. I did that to avoid profiling Thread.sleep(). The result is the same. I tried to reduce adaptive_min_method_invocation_count and adaptive_max_average_method_time_ns, and the result is the same. For CPU sampling, I tried to reduce the sampling period (thus increasing the event frequency) and the same result occurs.

OK, the problem is not related to YourKit. By default, classes org.eclipse.* are filtered. In my case, the code is actually in that namespace. Therefore, the solution is to uncheck Eclipse classes from the filter in the menu Settings -> Filters...